An integrated encyclopedia of DNA elements in the human genome.

Publication Type:

Journal Article



Nature, Volume 489, Issue 7414, p.57-74 (2012)


2012, Alleles, Animals, Binding Sites, Center-Authored Paper, chromatin, Chromatin Immunoprecipitation, Chromosomes, Human, Clinical Research Division, Comparative Medicine Core Facility, Deoxyribonuclease I, DNA, DNA Footprinting, DNA Methylation, DNA-Binding Proteins, Encyclopedias as Topic, Exons, Flow Cytometry Core Facility, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, Genome-Wide Association Study, GENOMICS, Histones, Humans, MAMMALS, Molecular Sequence Annotation, Neoplasms, Polymorphism, Single Nucleotide, Promoter Regions, Genetic, PROTEINS, Regulatory Sequences, Nucleic Acid, Sequence Analysis, RNA, Shared Resources, TRANSCRIPTION FACTORS, Transcription, Genetic


The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.